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Bio::DB::CacheServer::SeqDB
Caching DB object

Bio::DB::CacheServer::SeqDB - Caching DB object


NAME

Bio::DB::CacheServer::SeqDB - Caching DB object


SYNOPSIS

Give standard usage here


DESCRIPTION

Bio::DB::SeqI implmenting object which implements a cache via a bioperl-db database handle


FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.


  bioperl-l@bio.perl.org

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:


  bioperl-bugs@bio.perl.org

  http://bio.perl.org/bioperl-bugs/


AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

Describe contact details here


APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


Methods inherieted from Bio::DB::RandomAccessI

get_Seq_by_id


 Title   : get_Seq_by_id

 Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')

 Function: Gets a Bio::Seq object by its name

 Returns : a Bio::Seq object

 Args    : the id (as a string) of a sequence

 Throws  : "id does not exist" exception

get_Seq_by_acc


 Title   : get_Seq_by_acc

 Usage   : $seq = $db->get_Seq_by_acc('X77802');

 Function: Gets a Bio::Seq object by accession number

 Returns : A Bio::Seq object

 Args    : accession number (as a string)

 Throws  : "acc does not exist" exception


Methods [that were] specific for Bio::DB::SeqI

get_PrimarySeq_stream


 Title   : get_PrimarySeq_stream

 Usage   : $stream = get_PrimarySeq_stream

 Function: Makes a Bio::DB::SeqStreamI compliant object

           which provides a single method, next_primary_seq

 Returns : Bio::DB::SeqStreamI

 Args    : none

get_all_primary_ids


 Title   : get_all_ids

 Usage   : @ids = $seqdb->get_all_primary_ids()

 Function: gives an array of all the primary_ids of the 

           sequence objects in the database. These

           maybe ids (display style) or accession numbers

           or something else completely different - they

           *are not* meaningful outside of this database

           implementation.

 Example :

 Returns : an array of strings

 Args    : none

get_Seq_by_primary_id


 Title   : get_Seq_by_primary_id

 Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);

 Function: Gets a Bio::Seq object by the primary id. The primary

           id in these cases has to come from $db->get_all_primary_ids.

           There is no other way to get (or guess) the primary_ids

           in a database.

           The other possibility is to get Bio::PrimarySeqI objects

           via the get_PrimarySeq_stream and the primary_id field

           on these objects are specified as the ids to use here.

 Returns : A Bio::Seq object

 Args    : accession number (as a string)

 Throws  : "acc does not exist" exception

Get/Sets for attributed stored in this object

seq_adaptor


 Title   : seq_adaptor

 Usage   : $obj->seq_adaptor($newval)

 Function: 

 Example : 

 Returns : value of seq_adaptor

 Args    : newvalue (optional)

db_adaptor


 Title   : db_adaptor

 Usage   : $obj->db_adaptor($newval)

 Function: 

 Example : 

 Returns : value of db_adaptor

 Args    : newvalue (optional)

dbid


 Title   : dbid

 Usage   : $obj->dbid($newval)

 Function: 

 Example : 

 Returns : value of dbid

 Args    : newvalue (optional)

read_db


 Title   : read_db

 Usage   : $obj->read_db($newval)

 Function: 

 Example : 

 Returns : value of read_db

 Args    : newvalue (optional)
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